SYNOPSIS
gt ltrdigest [option ...] gff3_file
DESCRIPTION
-outfileprefix [string]
- prefix for output files (e.g. foo will create files called foo_*.csv and foo_*.fas) Omit this option for GFF3 output only.
-metadata [yes|no]
- output metadata (run conditions) to separate file (default: yes)
-seqnamelen [value]
- set maximal length of sequence names in FASTA headers (e.g. for clustalw or similar tools) (default: 20)
-pptlen [start end]
- required PPT length range (default: [8..30])
-uboxlen [start end]
- required U-box length range (default: [3..30])
-uboxdist [value]
- allowed U-box distance range from PPT (default: 0)
-pptradius [value]
- radius around beginning of 3' LTR to search for PPT (default: 30)
-pptrprob [value]
- purine emission probability inside PPT (default: 0.970000)
-pptyprob [value]
- pyrimidine emission probability inside PPT (default: 0.030000)
-pptgprob [value]
- background G emission probability outside PPT (default: 0.250000)
-pptcprob [value]
- background C emission probability outside PPT (default: 0.250000)
-pptaprob [value]
- background A emission probability outside PPT (default: 0.250000)
-ppttprob [value]
- background T emission probability outside PPT (default: 0.250000)
-pptuprob [value]
- U/T emission probability inside U-box (default: 0.910000)
-trnas [filename]
- tRNA library in multiple FASTA format for PBS detection Omit this option to disable PBS search.
-pbsalilen [start end]
- required PBS/tRNA alignment length range (default: [11..30])
-pbsoffset [start end]
- allowed PBS offset from LTR boundary range (default: [0..5])
-pbstrnaoffset [start end]
- allowed PBS/tRNA 3' end alignment offset range (default: [0..5])
-pbsmaxedist [value]
- maximal allowed PBS/tRNA alignment unit edit distance (default: 1)
-pbsradius [value]
- radius around end of 5' LTR to search for PBS (default: 30)
-hmms
- profile HMM models for domain detection (separate by spaces, finish with --) in HMMER3 format Omit this option to disable pHMM search.
-pdomevalcutoff [value]
- global E-value cutoff for pHMM search default 1E-6
-pdomcutoff [...]
- model-specific score cutoff choose from TC (trusted cutoff) | GA (gathering cutoff) | NONE (no cutoffs) (default: NONE)
-aliout [yes|no]
- output pHMM to amino acid sequence alignments (default: no)
-aaout [yes|no]
- output amino acid sequences for protein domain hits (default: no)
-allchains [yes|no]
- output features from all chains and unchained features, labeled with chain numbers (default: no)
-maxgaplen [value]
- maximal allowed gap size between fragments (in amino acids) when chaining pHMM hits for a protein domain (default: 50)
-force_recreate [yes|no]
- force recreation of hmmpressed profiles (default: no)
-pbsmatchscore [value]
- match score for PBS/tRNA alignments (default: 5)
-pbsmismatchscore [value]
- mismatch score for PBS/tRNA alignments (default: -10)
-pbsinsertionscore [value]
- insertion score for PBS/tRNA alignments (default: -20)
-pbsdeletionscore [value]
- deletion score for PBS/tRNA alignments (default: -20)
-v [yes|no]
- be verbose (default: no)
-o [filename]
- redirect output to specified file (default: undefined)
-gzip [yes|no]
- write gzip compressed output file (default: no)
-bzip2 [yes|no]
- write bzip2 compressed output file (default: no)
-force [yes|no]
- force writing to output file (default: no)
-seqfile [filename]
- set the sequence file from which to take the sequences (default: undefined)
-encseq [filename]
- set the encoded sequence indexname from which to take the sequences (default: undefined)
-seqfiles
- set the sequence files from which to extract the features use -- to terminate the list of sequence files
-matchdesc [yes|no]
- search the sequence descriptions from the input files for the desired sequence IDs (in GFF3), reporting the first match (default: no)
-matchdescstart [yes|no]
- exactly match the sequence descriptions from the input files for the desired sequence IDs (in GFF3) from the beginning to the first whitespace (default: no)
-usedesc [yes|no]
- use sequence descriptions to map the sequence IDs (in GFF3) to actual sequence entries. If a description contains a sequence range (e.g., III:1000001..2000000), the first part is used as sequence ID (III) and the first range position as offset (1000001) (default: no)
-regionmapping [string]
- set file containing sequence-region to sequence file mapping (default: undefined)
-help
- display help for basic options and exit
-help+
- display help for all options and exit
-version
- display version information and exit